7RTM | pdb_00007rtm

Cryo-EM Structure of the Sodium-driven Chloride/Bicarbonate Exchanger NDCBE (SLC4A8)

• PDB DOI: https://doi.org/10.2210/pdb7RTM/pdb
• EM Map EMD-24683: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Oryctolagus cuniculus
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2021-08-13 Released: 2021-09-29 
• Deposition Author(s): Wang, W.G., Tsirulnikov, K., Zhekova, H., Kayik, G., Muhammad-Khan, H., Azimov, R., Abuladze, N., Kao, L., Newman, D., Noskov, S.Y., Zhou, Z.H., Pushkin, A., Kurtz, I.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the sodium-driven chloride/bicarbonate exchanger NDCBE.

Wang, W., Tsirulnikov, K., Zhekova, H.R., Kayik, G., Khan, H.M., Azimov, R., Abuladze, N., Kao, L., Newman, D., Noskov, S.Y., Zhou, Z.H., Pushkin, A., Kurtz, I.

(2021) Nat Commun 12: 5690-5690

• PubMed: 34584093 
• DOI: https://doi.org/10.1038/s41467-021-25998-2
• Primary Citation Related Structures: 
  7RTM


• PubMed Abstract: 
  

  SLC4 transporters play significant roles in pH regulation and cellular sodium transport. The previously solved structures of the outward facing (OF) conformation for AE1 (SLC4A1) and NBCe1 (SLC4A4) transporters revealed an identical overall fold despite their different transport modes (chloride/bicarbonate exchange versus sodium-carbonate cotransport). However, the exact mechanism determining the different transport modes in the SLC4 family remains unknown. In this work, we report the cryo-EM 3.4 Å structure of the OF conformation of NDCBE (SLC4A8), which shares transport properties with both AE1 and NBCe1 by mediating the electroneutral exchange of sodium-carbonate with chloride. This structure features a fully resolved extracellular loop 3 and well-defined densities corresponding to sodium and carbonate ions in the tentative substrate binding pocket. Further, we combine computational modeling with functional studies to unravel the molecular determinants involved in NDCBE and SLC4 transport.

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Organizational Affiliation: 
• Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
Electron Imaging Center for Nanomachines, California NanoSystems Institute, University of California, Los Angeles, CA, USA.
Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada.
Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA.
Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. [e-mail].
Brain Research Institute, University of California, Los Angeles, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 130.47 kDa 
• Atom Count: 9,161 
• Modeled Residue Count: 1,142 
• Deposited Residue Count: 1,142 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Electroneutral sodium bicarbonate exchanger 1	A, B	571	Oryctolagus cuniculus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q6RVG2 (Rattus norvegicus) Explore Q6RVG2  Go to UniProtKB:  Q6RVG2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	3		N/A
Glycosylation Resources
GlyTouCan: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CO3 (Subject of Investigation/LOI)	G [auth A], J [auth B]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
NA (Subject of Investigation/LOI)	F [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	Coot	0.8.9
MODEL REFINEMENT	PHENIX	1.18.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-29 
Deposition Author(s): Wang, W.G., Tsirulnikov, K., Zhekova, H., Kayik, G., Muhammad-Khan, H., Azimov, R., Abuladze, N., Kao, L., Newman, D., Noskov, S.Y., Zhou, Z.H., Pushkin, A., Kurtz, I.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01 DK077162
Other government	Canada	No. RGPIN-2021-02439

Revision History  

• Version 1.0: 2021-09-29
  Type: Initial release
  
• Version 1.1: 2021-10-06
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary